Mitochondria are dynamic organelles that can change their morphology. The role of these mitochondrial dynamics in cardiomyocytes remains obscure in patients with heart failure (HF). Endomyocardial biopsies were performed consecutively in 127 HF patients, and mitochondrial morphology data were obtained from 111 patients by electron microscopy. The patients were divided into three groups according to mitochondrial area quartiles (fission [Q1, area ≤ 0.119 μm, n = 27], normal [Q2/Q3, 0.120 μm ≤ area ≤ 0.178 μm, n = 55], and fusion [Q4, area ≥ 0.179 μm, n = 28]). In the fission group, the serum N-terminal pro-brain natriuretic peptide and B-type natriuretic peptide (BNP) levels were significantly higher, and patients with HF and a reduced left ventricular ejection fraction were more common, than in the other groups. A multivariate logistic regression model showed that diabetes mellitus was independently associated with placement in the fission group (odds ratio: 2.835, 95%confidence interval [CI]: 1.037-7.752). A Kaplan-Meier curve analysis showed that the prognosis was significantly poorer in the fission group than in the other groups, and a multivariate Cox regression model revealed fission to be an independent predictor of 1500-day mortality (hazard ratio: 4.365, 95%CI: 1.198-15.909). The circulating levels of miR-140-5p (≥2500) were independently associated with the presence of mitochondrial fission (OR: 3.622, 95%CI: 1.260-10.413). Excessive mitochondrial fission was observed in patients with severe HF status, and was independently associated with adverse outcomes in HF patients. Circulating mitochondrial dynamics-related miRNA levels might be of use in detecting mitochondrial fission in the cardiomyocytes of HF patients.